Inflammatory bowel disease (IBD) is a term for a group of poorly understood gastrointestinal (GI) diseases of cats. Cats with IBD have uncontrolled intestinal inflammation but the inciting causes are poorly understood. This study was designed to evaluate the relationship of intestinal mucosal bacteria to inflammation and clinical signs in cats with IBD. Biopsies of the duodenum were obtained from 27 cats: 17 cats sampled as part of diagnostic investigation for GI disease, and 10 control cats. The number of Enterobacteriaceae was higher in cats with clinical signs of GI disease than healthy cats. Total numbers of mucosal bacteria were associated with changes in mucosal architecture and the degree of inflammation. The results of this study suggest that mucosal bacteria such as Enterobacteriaceae, E. coli and Clostridium are involved in the pathogenesis of IBD in cats.